Short instructions

This tutorial will explain you how to install the necessary R-packages for the MDAW hands-on sessions. Most of the scripts used in the tutorial build further from the package phyloseq, and hulp packages of Bioconductor and DADA2. To get started click on the menu’s on the left.

Five steps to get started

1. You need RStudio, and R-version 3.6.2 for windows, or R-version 3.6.3 for Mac. Execute the RStudio.exe, and also R3.6.2.exe, using the default settings.

2. Make a folder called MDAW e.g. in C:/Users/yourname/Documents. In this folder, place the MDAW.zip file and Unzip(“MDAW.zip”) it.

3. Go to the MDAW folder that you created in step 2. Right click on the file 1.Initialise.R and open with Rstudio. In RStudio, please first check if you are using R 3.6.2 version. For this click, Tools > Global Options > and in the pop-up screen select 64-bit, R 3.6.2. Click Apply, Ok. Now you are ready to run 1.initialise.R.
   Follow the instructions in the 1.Initialise.R file and execute all steps. When it is finished, it will automatically restart your R-session.
   The last command renv:restore can take 0.5 hour because it will auto-install all packages needed for the workshop, in the meantime you can watch this 15 min video to learn the basics of R.

4. Go to your MDAW folder, and open 2.Setup.R (right click and select open with Rstudio). Follow the instructions in the 2.Setup.R file, the script will create folders where all your results will be stored. When it is finished (2 min), you will get the message ‘succes’.

5. Now you are ready to run the scripts provided to you by the workshop speakers! For example, for the first hands-on, go to your MDAW folder, and open 3.RUN_DADA2.R. Follow the instructor on how to run the code.

Configuration

rm(list=ls()) # remove all objects from your workspace, start clean
     options(warn=-1) # toggle off warnings

renv::settings$snapshot.type("all")
     renv::snapshot()